data_Q56
#
_chem_comp.id Q56
_chem_comp.name "N~2~-{[(naphthalen-2-yl)methoxy]carbonyl}-N-{(2S)-1-oxo-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-leucinamide"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C25 H33 N3 O8 S"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2022-01-19
_chem_comp.pdbx_modified_date 2024-09-27
_chem_comp.pdbx_ambiguous_flag N
_chem_comp.pdbx_release_status REL
_chem_comp.pdbx_replaced_by ?
_chem_comp.pdbx_replaces ?
_chem_comp.formula_weight 535.610
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code Q56
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag Y
_chem_comp.pdbx_ideal_coordinates_details Corina
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 7TIX
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
_chem_comp.pdbx_pcm Y
#
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.alt_atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.charge
_chem_comp_atom.pdbx_align
_chem_comp_atom.pdbx_aromatic_flag
_chem_comp_atom.pdbx_leaving_atom_flag
_chem_comp_atom.pdbx_stereo_config
_chem_comp_atom.pdbx_backbone_atom_flag
_chem_comp_atom.pdbx_n_terminal_atom_flag
_chem_comp_atom.pdbx_c_terminal_atom_flag
_chem_comp_atom.model_Cartn_x
_chem_comp_atom.model_Cartn_y
_chem_comp_atom.model_Cartn_z
_chem_comp_atom.pdbx_model_Cartn_x_ideal
_chem_comp_atom.pdbx_model_Cartn_y_ideal
_chem_comp_atom.pdbx_model_Cartn_z_ideal
_chem_comp_atom.pdbx_component_atom_id
_chem_comp_atom.pdbx_component_comp_id
_chem_comp_atom.pdbx_ordinal
Q56 C16 C1 C 0 1 N N N N N N 6.408 1.311 25.592 0.774 1.067 -3.282 C16 Q56 1
Q56 C12 C2 C 0 1 N N S N N N 7.900 3.100 19.837 -4.103 -1.782 -0.705 C12 Q56 2
Q56 C14 C3 C 0 1 N N S N N N 7.448 0.197 23.525 -0.226 0.609 -1.039 C14 Q56 3
Q56 C15 C4 C 0 1 N N N N N N 7.635 1.185 24.672 -0.289 0.265 -2.528 C15 Q56 4
Q56 C17 C5 C 0 1 N N N N N N 5.556 0.053 25.724 0.796 0.633 -4.749 C17 Q56 5
Q56 C18 C6 C 0 1 N N N N N N 6.855 1.777 26.974 0.444 2.559 -3.197 C18 Q56 6
Q56 C22 C7 C 0 1 N N N N N N 8.947 -4.286 22.803 4.448 1.456 -0.219 C22 Q56 7
Q56 C23 C8 C 0 1 Y N N N N N 10.125 -4.086 21.840 5.673 0.834 0.401 C23 Q56 8
Q56 C25 C9 C 0 1 Y N N N N N 11.997 -2.793 21.020 7.633 -0.523 0.213 C25 Q56 9
Q56 C26 C10 C 0 1 Y N N N N N 12.804 -1.659 21.082 8.501 -1.330 -0.543 C26 Q56 10
Q56 C27 C11 C 0 1 Y N N N N N 13.864 -1.504 20.188 9.599 -1.875 0.047 C27 Q56 11
Q56 C29 C12 C 0 1 Y N N N N N 13.307 -3.616 19.160 9.060 -0.872 2.157 C29 Q56 12
Q56 C10 C13 C 0 1 N N N N N N 7.767 -1.435 17.725 -5.714 2.665 0.909 C10 Q56 13
Q56 C2 C14 C 0 1 N N N N N N 8.220 0.712 22.299 -1.350 -0.086 -0.315 C2 Q56 14
Q56 C20 C15 C 0 1 N N N N N N 8.072 -2.157 23.157 2.143 0.958 -0.585 C20 Q56 15
Q56 C24 C16 C 0 1 Y N N N N N 10.938 -2.949 21.906 6.490 0.058 -0.362 C24 Q56 16
Q56 C28 C17 C 0 1 Y N N N N N 14.120 -2.482 19.228 9.877 -1.647 1.394 C28 Q56 17
Q56 C30 C18 C 0 1 Y N N N N N 12.247 -3.769 20.055 7.917 -0.290 1.582 C30 Q56 18
Q56 C31 C19 C 0 1 Y N N N N N 11.443 -4.902 19.990 7.055 0.525 2.335 C31 Q56 19
Q56 C32 C20 C 0 1 Y N N N N N 10.387 -5.062 20.884 5.954 1.067 1.745 C32 Q56 20
Q56 C4 C21 C 0 1 N N S N N N 8.214 1.614 20.045 -3.723 -0.506 0.049 C4 Q56 21
Q56 C5 C22 C 0 1 N N N N N N 7.717 0.790 18.848 -4.935 0.424 0.121 C5 Q56 22
Q56 C6 C23 C 0 1 N N S N N N 8.202 -0.700 18.939 -4.572 1.673 0.928 C6 Q56 23
Q56 C7 C24 C 0 1 N N N N N N 9.705 -0.757 18.992 -4.401 1.320 2.423 C7 Q56 24
Q56 C8 C25 C 0 1 N N N N N N 10.034 -1.999 18.097 -4.983 2.575 3.112 C8 Q56 25
Q56 N19 N1 N 0 1 N N N N N N 7.988 -1.083 23.949 1.057 0.165 -0.488 N19 Q56 26
Q56 N3 N2 N 0 1 N N N N N N 7.535 1.135 21.234 -2.629 0.169 -0.655 N3 Q56 27
Q56 N9 N3 N 0 1 N N N N N N 8.774 -2.161 17.236 -5.925 3.150 2.145 N9 Q56 28
Q56 O1 O1 O 0 1 N N N N N N 9.426 0.752 22.291 -1.104 -0.874 0.573 O1 Q56 29
Q56 O11 O2 O 0 1 N N N N N N 6.669 -1.379 17.255 -6.343 2.981 -0.079 O11 Q56 30
Q56 O13 O3 O 0 1 N N N N N N 8.470 3.717 18.968 -2.950 -2.614 -0.847 O13 Q56 31
Q56 O21 O4 O 0 1 N N N N N N 8.751 -3.180 23.655 3.322 0.550 -0.079 O21 Q56 32
Q56 O33 O5 O 0 1 N N N N N N 7.579 -2.190 22.054 2.057 2.042 -1.128 O33 Q56 33
Q56 H1 H1 H 0 1 N N N N N N 5.766 2.099 25.172 1.752 0.885 -2.835 H1 Q56 34
Q56 H2 H2 H 0 1 N N N N N N 6.916 3.413 20.215 -4.486 -1.521 -1.691 H2 Q56 35
Q56 H3 H3 H 0 1 N N N N N N 6.379 0.109 23.279 -0.323 1.687 -0.910 H3 Q56 36
Q56 H4 H4 H 0 1 N N N N N N 8.490 0.853 25.279 -1.276 0.515 -2.917 H4 Q56 37
Q56 H5 H5 H 0 1 N N N N N N 7.851 2.175 24.245 -0.103 -0.800 -2.663 H5 Q56 38
Q56 H6 H6 H 0 1 N N N N N N 4.711 0.251 26.400 1.554 1.204 -5.286 H6 Q56 39
Q56 H7 H7 H 0 1 N N N N N N 5.174 -0.236 24.734 1.032 -0.430 -4.810 H7 Q56 40
Q56 H8 H8 H 0 1 N N N N N N 6.169 -0.764 26.133 -0.181 0.814 -5.196 H8 Q56 41
Q56 H9 H9 H 0 1 N N N N N N 5.978 1.867 27.632 -0.533 2.740 -3.644 H9 Q56 42
Q56 H10 H10 H 0 1 N N N N N N 7.558 1.045 27.398 0.428 2.868 -2.151 H10 Q56 43
Q56 H11 H11 H 0 1 N N N N N N 7.351 2.755 26.888 1.201 3.130 -3.734 H11 Q56 44
Q56 H12 H12 H 0 1 N N N N N N 8.032 -4.443 22.213 4.223 2.396 0.284 H12 Q56 45
Q56 H13 H13 H 0 1 N N N N N N 9.143 -5.176 23.420 4.633 1.645 -1.277 H13 Q56 46
Q56 H14 H14 H 0 1 N N N N N N 12.609 -0.898 21.823 8.297 -1.516 -1.587 H14 Q56 47
Q56 H15 H15 H 0 1 N N N N N N 14.488 -0.624 20.240 10.264 -2.495 -0.536 H15 Q56 48
Q56 H16 H16 H 0 1 N N N N N N 13.499 -4.374 18.415 9.288 -0.704 3.199 H16 Q56 49
Q56 H17 H17 H 0 1 N N N N N N 10.742 -2.190 22.649 6.261 -0.111 -1.404 H17 Q56 50
Q56 H18 H18 H 0 1 N N N N N N 14.944 -2.363 18.540 10.755 -2.092 1.839 H18 Q56 51
Q56 H19 H19 H 0 1 N N N N N N 11.638 -5.659 19.245 7.263 0.717 3.377 H19 Q56 52
Q56 H20 H20 H 0 1 N N N N N N 9.770 -5.947 20.835 5.290 1.687 2.329 H20 Q56 53
Q56 H21 H21 H 0 1 N N N N N N 9.302 1.484 20.147 -3.401 -0.763 1.059 H21 Q56 54
Q56 H22 H22 H 0 1 N N N N N N 8.104 1.237 17.920 -5.229 0.716 -0.887 H22 Q56 55
Q56 H23 H23 H 0 1 N N N N N N 6.617 0.808 18.833 -5.762 -0.094 0.606 H23 Q56 56
Q56 H24 H24 H 0 1 N N N N N N 7.775 -1.164 19.840 -3.664 2.129 0.535 H24 Q56 57
Q56 H25 H25 H 0 1 N N N N N N 10.060 -0.905 20.022 -4.976 0.431 2.683 H25 Q56 58
Q56 H26 H26 H 0 1 N N N N N N 10.152 0.159 18.579 -3.349 1.189 2.675 H26 Q56 59
Q56 H27 H27 H 0 1 N N N N N N 10.207 -2.893 18.713 -5.505 2.295 4.027 H27 Q56 60
Q56 H28 H28 H 0 1 N N N N N N 10.918 -1.809 17.470 -4.188 3.286 3.334 H28 Q56 61
Q56 H29 H29 H 0 1 N N N N N N 8.317 -1.166 24.890 1.125 -0.700 -0.055 H29 Q56 62
Q56 H30 H30 H 0 1 N N N N N N 6.535 1.121 21.256 -2.826 0.800 -1.365 H30 Q56 63
Q56 H31 H31 H 0 1 N N N N N N 8.716 -2.734 16.418 -6.613 3.797 2.369 H31 Q56 64
Q56 S1 S1 S 0 1 N Y N N N N ? ? ? -5.381 -2.675 0.223 S1 Q56 65
Q56 O2 O6 O 0 1 N Y N N N N ? ? ? -5.776 -3.848 -0.475 O2 Q56 66
Q56 O4 O7 O 0 1 N Y N N N N ? ? ? -5.055 -2.719 1.605 O4 Q56 67
Q56 O3 O8 O 0 1 N Y N N N N ? ? ? -6.602 -1.769 0.154 O3 Q56 68
Q56 H32 H32 H 0 1 N N N N N N 8.167 4.617 18.968 -2.224 -2.200 -1.334 H32 Q56 69
Q56 H33 H33 H 0 1 N Y N N N N ? ? ? -7.378 -2.119 0.614 H33 Q56 70
#
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_aromatic_flag
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_ordinal
Q56 N9 C10 SING N N 1
Q56 N9 C8 SING N N 2
Q56 O11 C10 DOUB N N 3
Q56 C10 C6 SING N N 4
Q56 C8 C7 SING N N 5
Q56 C5 C6 SING N N 6
Q56 C5 C4 SING N N 7
Q56 C6 C7 SING N N 8
Q56 O13 C12 SING N N 9
Q56 C29 C28 DOUB Y N 10
Q56 C29 C30 SING Y N 11
Q56 C28 C27 SING Y N 12
Q56 C12 C4 SING N N 13
Q56 C31 C30 DOUB Y N 14
Q56 C31 C32 SING Y N 15
Q56 C4 N3 SING N N 16
Q56 C30 C25 SING Y N 17
Q56 C27 C26 DOUB Y N 18
Q56 C32 C23 DOUB Y N 19
Q56 C25 C26 SING Y N 20
Q56 C25 C24 DOUB Y N 21
Q56 N3 C2 SING N N 22
Q56 C23 C24 SING Y N 23
Q56 C23 C22 SING N N 24
Q56 O33 C20 DOUB N N 25
Q56 O1 C2 DOUB N N 26
Q56 C2 C14 SING N N 27
Q56 C22 O21 SING N N 28
Q56 C20 O21 SING N N 29
Q56 C20 N19 SING N N 30
Q56 C14 N19 SING N N 31
Q56 C14 C15 SING N N 32
Q56 C15 C16 SING N N 33
Q56 C16 C17 SING N N 34
Q56 C16 C18 SING N N 35
Q56 C16 H1 SING N N 36
Q56 C12 H2 SING N N 37
Q56 C14 H3 SING N N 38
Q56 C15 H4 SING N N 39
Q56 C15 H5 SING N N 40
Q56 C17 H6 SING N N 41
Q56 C17 H7 SING N N 42
Q56 C17 H8 SING N N 43
Q56 C18 H9 SING N N 44
Q56 C18 H10 SING N N 45
Q56 C18 H11 SING N N 46
Q56 C22 H12 SING N N 47
Q56 C22 H13 SING N N 48
Q56 C26 H14 SING N N 49
Q56 C27 H15 SING N N 50
Q56 C29 H16 SING N N 51
Q56 C24 H17 SING N N 52
Q56 C28 H18 SING N N 53
Q56 C31 H19 SING N N 54
Q56 C32 H20 SING N N 55
Q56 C4 H21 SING N N 56
Q56 C5 H22 SING N N 57
Q56 C5 H23 SING N N 58
Q56 C6 H24 SING N N 59
Q56 C7 H25 SING N N 60
Q56 C7 H26 SING N N 61
Q56 C8 H27 SING N N 62
Q56 C8 H28 SING N N 63
Q56 N19 H29 SING N N 64
Q56 N3 H30 SING N N 65
Q56 N9 H31 SING N N 66
Q56 C12 S1 SING N N 67
Q56 S1 O2 DOUB N N 68
Q56 S1 O4 DOUB N N 69
Q56 S1 O3 SING N N 70
Q56 O13 H32 SING N N 71
Q56 O3 H33 SING N N 72
#
loop_
_pdbx_chem_comp_descriptor.comp_id
_pdbx_chem_comp_descriptor.type
_pdbx_chem_comp_descriptor.program
_pdbx_chem_comp_descriptor.program_version
_pdbx_chem_comp_descriptor.descriptor
Q56 SMILES ACDLabs 12.01 "CC(C)CC(NC(=O)OCc1cc2ccccc2cc1)C(=O)NC(CC1CCNC1=O)C(O)S(=O)(=O)O"
Q56 InChI InChI 1.03 "InChI=1S/C25H33N3O8S/c1-15(2)11-20(28-25(32)36-14-16-7-8-17-5-3-4-6-18(17)12-16)23(30)27-21(24(31)37(33,34)35)13-19-9-10-26-22(19)29/h3-8,12,15,19-21,24,31H,9-11,13-14H2,1-2H3,(H,26,29)(H,27,30)(H,28,32)(H,33,34,35)/t19-,20-,21-,24-/m0/s1"
Q56 InChIKey InChI 1.03 KLDKNBLMZUYYLD-CIEVZJJWSA-N
Q56 SMILES_CANONICAL CACTVS 3.385 "CC(C)C[C@H](NC(=O)OCc1ccc2ccccc2c1)C(=O)N[C@@H](C[C@@H]3CCNC3=O)[C@@H](O)[S](O)(=O)=O"
Q56 SMILES CACTVS 3.385 "CC(C)C[CH](NC(=O)OCc1ccc2ccccc2c1)C(=O)N[CH](C[CH]3CCNC3=O)[CH](O)[S](O)(=O)=O"
Q56 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC(C)C[C@@H](C(=O)N[C@@H](C[C@@H]1CCNC1=O)[C@H](O)S(=O)(=O)O)NC(=O)OCc2ccc3ccccc3c2"
Q56 SMILES "OpenEye OEToolkits" 2.0.7 "CC(C)CC(C(=O)NC(CC1CCNC1=O)C(O)S(=O)(=O)O)NC(=O)OCc2ccc3ccccc3c2"
#
loop_
_pdbx_chem_comp_identifier.comp_id
_pdbx_chem_comp_identifier.type
_pdbx_chem_comp_identifier.program
_pdbx_chem_comp_identifier.program_version
_pdbx_chem_comp_identifier.identifier
Q56 "SYSTEMATIC NAME" ACDLabs 12.01 "(1S,2S)-1-hydroxy-2-[(N-{[(naphthalen-2-yl)methoxy]carbonyl}-L-leucyl)amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid"
Q56 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(1~{R},2~{S})-2-[[(2~{S})-4-methyl-2-(naphthalen-2-ylmethoxycarbonylamino)pentanoyl]amino]-1-oxidanyl-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propane-1-sulfonic acid"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
Q56 "Create component" 2022-01-19 RCSB
Q56 "Initial release" 2022-05-04 RCSB
Q56 "Modify PCM" 2024-09-27 PDBE
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id Q56
_pdbx_chem_comp_pcm.modified_residue_id CYS
_pdbx_chem_comp_pcm.type None
_pdbx_chem_comp_pcm.category "Covalent chemical modification"
_pdbx_chem_comp_pcm.position "Amino-acid side chain"
_pdbx_chem_comp_pcm.polypeptide_position "Any position"
_pdbx_chem_comp_pcm.comp_id_linking_atom C12
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom SG
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ?
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ?
#